Joe Farman, who has died aged 82, was the leader of a small group of scientists who made one of the most important discoveries in recent history. In 1985, they published a landmark paper on the ozone layer, the protective skin that filters the sun's ultraviolet rays and without which the rays can cause cancers and eye damage. Their research showed that the ozone layer was being rapidly depleted over the Antarctic.

Just two years later, world governments signed the Montreal protocol, a treaty phasing out the use of CFCs, the chemicals used in aerosols and other applications that were reacting with the ozone. This swift action bore witness to the scale of the threat, and the protocol still stands as the most successful environmental treaty ever. Disaster was averted, and the dangerous chemicals were replaced by – somewhat – safer alternatives. Full repair of the ozone layer will still take decades – the gaps in the atmosphere should close by 2080, at current rates – but without the work of Farman the effects could have been catastrophic.

The story of the ozone layer is one of the most important lessons in modern science. Millions of tonnes of dangerous chemical compounds had been poured into the air from industrial activities over decades. Unknown to the people below, these chemicals were causing drastic changes to the atmosphere that were imperilling life on earth in ways barely understood. For years the damage went unnoticed.

Although work by the chemists Paul Crutzen, Mario Molina and others in the 1970s had shown that CFCs could react with ozone, there was no empirical evidence that such destruction was actually happening. Satellites from the US space agency Nasa had found nothing. It appeared, in the early 1980s, that fears for the ozone layer were unfounded.

When Farman ran his first readings from a primitive Dobson spectrometer, wrapped in a quilt in the Antarctic in the early 1980s, he thought the instrument must be wrong. The readings suggested a drastic drop in the levels of ozone above the south pole. He got a new machine, but it gave the same results.

Convinced, after nearly five years of careful research, he, Brian Gardiner and Jonathan Shanklin published their findings in the peer-review journal Nature on 16 May 1985. The results, showing a 40% drop in ozone, were explosive. It transpired that Nasa had failed to find the drastic drop because, although its satellites and instruments had detected the absence, its software was set to ignore such unusual readings.

In the teeth of strong opposition from the chemicals industries – which protested that the cost of replacing CFCs was too much to bear – the Montreal protocol forced a massive change. Ironically, one of the key groups of replacement chemicals was that of hydrofluorocarbons, later found to be greenhouse gases thousands of times more potent than carbon dioxide in warming the planet.

Crucially, Farman had the support of Margaret Thatcher, who was a former chemist and who championed his work and the Montreal protocol. Her support started before his key discoveries: Farman worked for the British Antarctic Survey, which had been threatened with savage reductions and possible closure under the Tories' cuts, and Thatcher saved the research establishment, ringfencing its budget, though not only for scientific reasons; the strategic value of a research outpost in the Antarctic was not lost on the victor of the Falklands war.

Farman was born in Norwich, the son of a builder and a primary school teacher, and with a sister eight years his senior. As a boy he spent his leisure time cycling the length and breadth of Norfolk, and as a member of the Scouts. A pupil of Norwich school, he won a scholarship to Corpus Christi College, Cambridge, where he studied natural sciences. After taking his degree, Farman joined De Havilland, then a major aircraft manufacturer.

In 1956, he saw an advertisement for people to practise physics in the Antarctic. It appealed to his sense of adventure – he answered the ad and got the job. There followed many years of research near the south pole, in what was at first called the Falkland Islands Dependency Survey and was later renamed the British Antarctic Survey.

In 1959 he met Paula Bowyer, an Oxford history graduate and teacher, and they married in 1971. They moved to Cambridge, to the British Antarctic Survey's laboratory headquarters, in 1976. He was elected a fellow of Corpus Christi College in 1989.

Farman continued to conduct research in Antarctica in later years, though he disparaged the comparative luxury that modern scientists enjoy. Once, in 1990, having set out on foot to retrieve some instruments, he was surprised to see a helicopter from another research centre land near him and offer him a lift. His reply is unrecorded.

Crutzen, Molina and F Sherwood Rowland were awarded the Nobel prize in 1995 for their work on CFCs. Farman and the team that found the data proving their hypothesis, and the danger to the planet, were not similarly honoured. But Farman won the Polar medal, the Society of Chemical Industry environment medal, the Chree medal and prize, and membership of the United Nations Global 500 roll of honour. He was appointed OBE in 1988 and CBE in 2000.

Always an active man, and a keen hockey and rugby player in his youth, Farman was to be seen every morning, until the day before he suffered a stroke in February, cycling to Cambridge University's chemistry department, which he joined after he retired from the civil service (to which the British Antarctic Survey belongs) at the age of 60. When not there, he was likely to be on his allotment, where he grew vegetables and experimented with methods to create compost.

He is survived by Paula.

• Joseph Charles Farman, geophysicist, born 7 August 1930; died 11 May 2013